Updating nf-core tools to version 2.1.

Updates

Removed the nf-core-biocontainers-temp role by moving the rnaseq pipeline download into the nf-core role.
Downloading singularity images using nf-core tools instead of singularity pull.
- Images that cannot be found in the NXF_SINGULARITY_CACHEDIR are downloaded.
Used the singularity.cacheDir instead of process.container in the pipeline specific configs since it can search in a directory for all associated images.
The singularity images of the pipelines using dsl2 and biocontainers (ampliseq, viralrecon, rnaseq) were all added to the same directory biocontainers to avoid downloading duplicates.
Changed the directory name for the nf-core virtual environment and set the nf-core tools version to 2.1.
Changed nf-core tools download flag release to revision since the flag changed name.
Updated nf-core tools, Nextflow and pipeline versions.
Merged master branch into bimonthly.

Version updates

methylseq (v1.6 (bimonthly) -> v1.6.1(master +thisPR))
ampliseq (v1.1.2 (bimonthly) -> v1.2.0 (master) -> v2.0.0(thisPR))
atacseq (v1.1.0 (bimonthly) -> v1.2.1 (master) -> v1.2.1 (thisPR))
viralrecon (v1.1.0 (bimonthly+master) -> v2.2 (thisPR))
rnaseq (3.0 (bimonthly+master) -> 3.3 (thisPR))
nf-core tools (1.7 (bimonthly+master) -> 2.1 (thisPR))
nextflow (v20.11.0-edge (master) -> v21.04.1 (bimonthly) -> v21.04.3 (thisPR))
archive_upload_version (v1.0.2 (bimonthly) -> v1.0.4 (master+thisPR))
multiqc (v1.10 (bimonthly) -> v1.10.1 (master+thisPR))